Extrusion along a curve: position of the profile
Without an image of some sort it's hard to guess, but this is a common enough problem that I think I know what you're facing.

If I understand you correctly, all you need to do is rotate the profile curve in edit mode, (instead of object mode) to align the axes of the profile with the axes of the other object.

The documentation is a little obtuse, but it might be helpful.